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Chromatin features of plant telomeric sequences at terminal vs. internal positions.

Majerová E, Mandáková T, Vu GT, Fajkus J, Lysak MA, Fojtová M - Front Plant Sci (2014)

Bottom Line: Chromatin of genuine telomeres displayed heterochromatic as well as euchromatic marks, while ITRs were just heterochromatic.Telomeric transcripts TERRA (G-rich) and ARRET (C-rich) were identified in both plants and their levels varied among tissues with a maximum in blossoms.Plants with substantially different proportions of internally and terminally located telomeric repeats are instrumental in clarifying the chromatin status of telomeric repeats at distinct chromosome locations.

View Article: PubMed Central - PubMed

Affiliation: Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology and Faculty of Science, Masaryk University Brno, Czech Republic.

ABSTRACT
Epigenetic mechanisms are involved in regulation of crucial cellular processes in eukaryotic organisms. Data on the epigenetic features of plant telomeres and their epigenetic regulation were published mostly for Arabidopsis thaliana, in which the presence of interstitial telomeric repeats (ITRs) may interfere with genuine telomeres in most analyses. Here, we studied the epigenetic landscape and transcription of telomeres and ITRs in Nicotiana tabacum with long telomeres and no detectable ITRs, and in Ballantinia antipoda with large blocks of pericentromeric ITRs and relatively short telomeres. Chromatin of genuine telomeres displayed heterochromatic as well as euchromatic marks, while ITRs were just heterochromatic. Methylated cytosines were present at telomeres and ITRs, but showed a bias with more methylation toward distal telomere positions and different blocks of B. antipoda ITRs methylated to different levels. Telomeric transcripts TERRA (G-rich) and ARRET (C-rich) were identified in both plants and their levels varied among tissues with a maximum in blossoms. Plants with substantially different proportions of internally and terminally located telomeric repeats are instrumental in clarifying the chromatin status of telomeric repeats at distinct chromosome locations.

No MeSH data available.


Analysis of histone modifications at genuine telomeres and ITRs in N. tabacum and B. antipoda. Chromatin was immunoprecipitated by antibodies against the euchromatic marks H3K4me3 and H3K9me3, heterochromatic marks H4K20me and H3K9me2 and the epigenetic mark for developmentally silenced regions H3K27me3, and hybridized with radioactively labeled probes. In tobacco, H3K9me2 and H3K27me3 signals were prevalent, followed by signal for H3K4me3. B. antipoda displayed both heterochromatin- (H3K9me2) and euchromatin-specific (H3K4me3) marks after hybridization with the telomeric pltel-C probe, but only the heterochromatic H3H9me2 mark was clearly above the detection limit after hybridization with the ITR probes Ba493 and Ba576.
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Figure 5: Analysis of histone modifications at genuine telomeres and ITRs in N. tabacum and B. antipoda. Chromatin was immunoprecipitated by antibodies against the euchromatic marks H3K4me3 and H3K9me3, heterochromatic marks H4K20me and H3K9me2 and the epigenetic mark for developmentally silenced regions H3K27me3, and hybridized with radioactively labeled probes. In tobacco, H3K9me2 and H3K27me3 signals were prevalent, followed by signal for H3K4me3. B. antipoda displayed both heterochromatin- (H3K9me2) and euchromatin-specific (H3K4me3) marks after hybridization with the telomeric pltel-C probe, but only the heterochromatic H3H9me2 mark was clearly above the detection limit after hybridization with the ITR probes Ba493 and Ba576.

Mentions: To investigate the epigenetic patterns of telomere repeat-containing chromatin at distinct genomic locations, ChIP analyses were carried out using antibodies against five specific histone modifications: H3K4me3 and H3K9me3 as euchromatic marks in plants, H4K20me1 and H3K9me2 as heterochromatic marks, and H3K27me3 as mark of developmentally silenced genes (reviewed in Berr et al., 2011). The telomere-specific probe pltel-C was applied for hybridization to address telomeric sequences; in B. antipoda additionally, Ba493 and Ba576 were used to address ITR regions. In accordance with the previous results for A. thaliana (Vrbsky et al., 2010), we found that tobacco telomeres were significantly enriched in H3K9me2 and H3K27me3 modifications, with a contribution of euchromatic H3K4me3 (Figure 5). Telomeric repeats of B. antipoda showed predominantly the heterochromatic mark H3K9me2, and a minor signal for H3K4me3. No H3K27me3 was detected within telomeric chromatin of B. antipoda. Hybridization with the ITR-specific probes Ba493 and Ba576 revealed only signals for H3K9me2 (Figure 5). Extensive mapping of chromatin states in A. thaliana showed that H3K9me2 and H3K4me3 marks are, in essence, mutually exclusive (Roudier et al., 2011). In this context, the association of both modifications with plant telomeres may indicate the existence of two distinct fractions of telomeric chromatin; the dominant heterochromatic fraction associated with H3K9me2 and the second one that is more euchromatin-like. We did not find any H3K9me3 signal suggesting different roles for H3K9 and H3K4 trimethylations at plant telomeres, although both these modifications frequently co-localized at euchromatic genes in A. thaliana (Roudier et al., 2011). Moreover, we did not detect H4K20me1 at tobacco telomeres, which is astonishing because the dominant plant telomeric mark H3K9me2 was found mainly at heterochromatic transposable elements and other repeats, and overlaps significantly with H4K20me1 in A. thaliana (Roudier et al., 2011). The high density of H3K9me2 (Roudier et al., 2011) suggests that these marks may occur independently of each other in distinct chromosome regions, and telomeres may represent such regions.


Chromatin features of plant telomeric sequences at terminal vs. internal positions.

Majerová E, Mandáková T, Vu GT, Fajkus J, Lysak MA, Fojtová M - Front Plant Sci (2014)

Analysis of histone modifications at genuine telomeres and ITRs in N. tabacum and B. antipoda. Chromatin was immunoprecipitated by antibodies against the euchromatic marks H3K4me3 and H3K9me3, heterochromatic marks H4K20me and H3K9me2 and the epigenetic mark for developmentally silenced regions H3K27me3, and hybridized with radioactively labeled probes. In tobacco, H3K9me2 and H3K27me3 signals were prevalent, followed by signal for H3K4me3. B. antipoda displayed both heterochromatin- (H3K9me2) and euchromatin-specific (H3K4me3) marks after hybridization with the telomeric pltel-C probe, but only the heterochromatic H3H9me2 mark was clearly above the detection limit after hybridization with the ITR probes Ba493 and Ba576.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
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Figure 5: Analysis of histone modifications at genuine telomeres and ITRs in N. tabacum and B. antipoda. Chromatin was immunoprecipitated by antibodies against the euchromatic marks H3K4me3 and H3K9me3, heterochromatic marks H4K20me and H3K9me2 and the epigenetic mark for developmentally silenced regions H3K27me3, and hybridized with radioactively labeled probes. In tobacco, H3K9me2 and H3K27me3 signals were prevalent, followed by signal for H3K4me3. B. antipoda displayed both heterochromatin- (H3K9me2) and euchromatin-specific (H3K4me3) marks after hybridization with the telomeric pltel-C probe, but only the heterochromatic H3H9me2 mark was clearly above the detection limit after hybridization with the ITR probes Ba493 and Ba576.
Mentions: To investigate the epigenetic patterns of telomere repeat-containing chromatin at distinct genomic locations, ChIP analyses were carried out using antibodies against five specific histone modifications: H3K4me3 and H3K9me3 as euchromatic marks in plants, H4K20me1 and H3K9me2 as heterochromatic marks, and H3K27me3 as mark of developmentally silenced genes (reviewed in Berr et al., 2011). The telomere-specific probe pltel-C was applied for hybridization to address telomeric sequences; in B. antipoda additionally, Ba493 and Ba576 were used to address ITR regions. In accordance with the previous results for A. thaliana (Vrbsky et al., 2010), we found that tobacco telomeres were significantly enriched in H3K9me2 and H3K27me3 modifications, with a contribution of euchromatic H3K4me3 (Figure 5). Telomeric repeats of B. antipoda showed predominantly the heterochromatic mark H3K9me2, and a minor signal for H3K4me3. No H3K27me3 was detected within telomeric chromatin of B. antipoda. Hybridization with the ITR-specific probes Ba493 and Ba576 revealed only signals for H3K9me2 (Figure 5). Extensive mapping of chromatin states in A. thaliana showed that H3K9me2 and H3K4me3 marks are, in essence, mutually exclusive (Roudier et al., 2011). In this context, the association of both modifications with plant telomeres may indicate the existence of two distinct fractions of telomeric chromatin; the dominant heterochromatic fraction associated with H3K9me2 and the second one that is more euchromatin-like. We did not find any H3K9me3 signal suggesting different roles for H3K9 and H3K4 trimethylations at plant telomeres, although both these modifications frequently co-localized at euchromatic genes in A. thaliana (Roudier et al., 2011). Moreover, we did not detect H4K20me1 at tobacco telomeres, which is astonishing because the dominant plant telomeric mark H3K9me2 was found mainly at heterochromatic transposable elements and other repeats, and overlaps significantly with H4K20me1 in A. thaliana (Roudier et al., 2011). The high density of H3K9me2 (Roudier et al., 2011) suggests that these marks may occur independently of each other in distinct chromosome regions, and telomeres may represent such regions.

Bottom Line: Chromatin of genuine telomeres displayed heterochromatic as well as euchromatic marks, while ITRs were just heterochromatic.Telomeric transcripts TERRA (G-rich) and ARRET (C-rich) were identified in both plants and their levels varied among tissues with a maximum in blossoms.Plants with substantially different proportions of internally and terminally located telomeric repeats are instrumental in clarifying the chromatin status of telomeric repeats at distinct chromosome locations.

View Article: PubMed Central - PubMed

Affiliation: Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology and Faculty of Science, Masaryk University Brno, Czech Republic.

ABSTRACT
Epigenetic mechanisms are involved in regulation of crucial cellular processes in eukaryotic organisms. Data on the epigenetic features of plant telomeres and their epigenetic regulation were published mostly for Arabidopsis thaliana, in which the presence of interstitial telomeric repeats (ITRs) may interfere with genuine telomeres in most analyses. Here, we studied the epigenetic landscape and transcription of telomeres and ITRs in Nicotiana tabacum with long telomeres and no detectable ITRs, and in Ballantinia antipoda with large blocks of pericentromeric ITRs and relatively short telomeres. Chromatin of genuine telomeres displayed heterochromatic as well as euchromatic marks, while ITRs were just heterochromatic. Methylated cytosines were present at telomeres and ITRs, but showed a bias with more methylation toward distal telomere positions and different blocks of B. antipoda ITRs methylated to different levels. Telomeric transcripts TERRA (G-rich) and ARRET (C-rich) were identified in both plants and their levels varied among tissues with a maximum in blossoms. Plants with substantially different proportions of internally and terminally located telomeric repeats are instrumental in clarifying the chromatin status of telomeric repeats at distinct chromosome locations.

No MeSH data available.